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EOS Package

The zalmoxis.eos package provides equation-of-state functionality organized by EOS family.

eos

EOS package for Zalmoxis.

Re-exports all public and private functions from the submodules so that from zalmoxis.eos import calculate_density works identically to the old monolithic eos_functions.py.

__all__ = ['load_paleos_table', 'load_paleos_unified_table', '_fast_bilinear', '_paleos_clamp_temperature', '_ensure_unified_cache', 'get_tabulated_eos', 'get_paleos_unified_density', 'get_paleos_unified_density_batch', '_get_paleos_unified_nabla_ad', 'load_melting_curve', 'get_solidus_liquidus_functions', 'get_Tdep_density', 'get_Tdep_material', '_get_paleos_nabla_ad', 'calculate_density', 'calculate_density_batch', 'compute_adiabatic_temperature', '_compute_paleos_dtdp', 'calculate_temperature_profile', 'create_pressure_density_files'] module-attribute

_compute_paleos_dtdp(pressure, temperature, mat_PALEOS, solidus_func, liquidus_func, interpolation_functions)

Compute dT/dP from PALEOS nabla_ad with phase-aware weighting.

Uses solid nabla_ad below solidus, liquid nabla_ad above liquidus, and melt-fraction-weighted average in the mushy zone.

Parameters:

Name Type Description Default
pressure float

Pressure in Pa.

required
temperature float

Temperature in K.

required
mat_PALEOS dict

PALEOS material properties dict.

required
solidus_func callable or None

Solidus melting curve interpolation function.

required
liquidus_func callable or None

Liquidus melting curve interpolation function.

required
interpolation_functions dict

Shared interpolation cache.

required

Returns:

Type Description
float or None

dT/dP in K/Pa, or None if lookup fails.

Source code in src/zalmoxis/eos/temperature.py
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def _compute_paleos_dtdp(
    pressure, temperature, mat_PALEOS, solidus_func, liquidus_func, interpolation_functions
):
    """Compute dT/dP from PALEOS nabla_ad with phase-aware weighting.

    Uses solid nabla_ad below solidus, liquid nabla_ad above liquidus,
    and melt-fraction-weighted average in the mushy zone.

    Parameters
    ----------
    pressure : float
        Pressure in Pa.
    temperature : float
        Temperature in K.
    mat_PALEOS : dict
        PALEOS material properties dict.
    solidus_func : callable or None
        Solidus melting curve interpolation function.
    liquidus_func : callable or None
        Liquidus melting curve interpolation function.
    interpolation_functions : dict
        Shared interpolation cache.

    Returns
    -------
    float or None
        dT/dP in K/Pa, or None if lookup fails.
    """
    if pressure <= 0 or temperature <= 0:
        return None

    # Determine phase
    T_sol = solidus_func(pressure) if solidus_func is not None else np.nan
    T_liq = liquidus_func(pressure) if liquidus_func is not None else np.nan

    if np.isnan(T_sol) or np.isnan(T_liq) or T_liq <= T_sol:
        # Outside melting curve range or degenerate: use solid table
        nabla = _get_paleos_nabla_ad(
            pressure, temperature, mat_PALEOS, 'solid_mantle', interpolation_functions
        )
    elif temperature <= T_sol:
        # Solid phase
        nabla = _get_paleos_nabla_ad(
            pressure, temperature, mat_PALEOS, 'solid_mantle', interpolation_functions
        )
    elif temperature >= T_liq:
        # Liquid phase
        nabla = _get_paleos_nabla_ad(
            pressure, temperature, mat_PALEOS, 'melted_mantle', interpolation_functions
        )
    else:
        # Mixed phase: melt-fraction-weighted nabla_ad
        phi = (temperature - T_sol) / (T_liq - T_sol)
        nabla_solid = _get_paleos_nabla_ad(
            pressure, temperature, mat_PALEOS, 'solid_mantle', interpolation_functions
        )
        nabla_liquid = _get_paleos_nabla_ad(
            pressure, temperature, mat_PALEOS, 'melted_mantle', interpolation_functions
        )
        if (
            nabla_solid is None and nabla_liquid is None
        ):  # pragma: no cover - both phases undefined; defensive
            return None
        if (
            nabla_solid is None
        ):  # pragma: no cover - solid-side phase undefined at table edge; defensive
            nabla = nabla_liquid
        elif (
            nabla_liquid is None
        ):  # pragma: no cover - liquid-side phase undefined at table edge; defensive
            nabla = nabla_solid
        else:
            nabla = (1.0 - phi) * nabla_solid + phi * nabla_liquid

    if nabla is None or nabla <= 0:  # pragma: no cover - non-positive nabla_ad; defensive
        return None

    # Convert: dT/dP = nabla_ad * T / P
    return nabla * temperature / pressure

_ensure_unified_cache(eos_file, interpolation_functions)

Ensure a unified PALEOS table is loaded into the interpolation cache.

Tries loading from a binary pickle cache first (fast), then falls back to the text table (slow). Saves a pickle cache after the first text load.

Parameters:

Name Type Description Default
eos_file str

Path to the unified PALEOS table file.

required
interpolation_functions dict

Shared interpolation cache.

required

Returns:

Type Description
dict

The cache entry for this file.

Source code in src/zalmoxis/eos/interpolation.py
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def _ensure_unified_cache(eos_file, interpolation_functions):
    """Ensure a unified PALEOS table is loaded into the interpolation cache.

    Tries loading from a binary pickle cache first (fast), then falls back
    to the text table (slow). Saves a pickle cache after the first text load.

    Parameters
    ----------
    eos_file : str
        Path to the unified PALEOS table file.
    interpolation_functions : dict
        Shared interpolation cache.

    Returns
    -------
    dict
        The cache entry for this file.
    """
    if eos_file not in interpolation_functions:
        import pickle

        cache_path = eos_file.replace('.dat', '.pkl')
        try:
            with open(cache_path, 'rb') as f:
                interpolation_functions[eos_file] = pickle.load(f)
            logger.debug('Loaded PALEOS cache from %s', cache_path)
        except (FileNotFoundError, EOFError, pickle.UnpicklingError):
            logger.info('Loading PALEOS table from text: %s', eos_file)
            interpolation_functions[eos_file] = load_paleos_unified_table(eos_file)
            # Save binary cache for next time
            try:
                with open(cache_path, 'wb') as f:
                    pickle.dump(interpolation_functions[eos_file], f, protocol=4)
                logger.info('Saved PALEOS binary cache: %s', cache_path)
            except OSError:
                logger.debug('Could not save cache to %s', cache_path)

    return interpolation_functions[eos_file]

_fast_bilinear(log_p, log_t, grid, cached)

O(1) bilinear interpolation on a log-uniform grid (scalar).

Optimized for the hot path: called ~2M times per structure solve. Uses direct floor indexing (no rounding, no max/min builtins).

Parameters:

Name Type Description Default
log_p float

log10 of pressure, already clamped to grid bounds.

required
log_t float

log10 of temperature, already clamped to valid range.

required
grid ndarray

2D array of values, shape (n_p, n_t).

required
cached dict

Cache entry with grid metadata.

required

Returns:

Type Description
float

Interpolated value. NaN if any corner is NaN.

Source code in src/zalmoxis/eos/interpolation.py
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def _fast_bilinear(log_p, log_t, grid, cached):
    """O(1) bilinear interpolation on a log-uniform grid (scalar).

    Optimized for the hot path: called ~2M times per structure solve.
    Uses direct floor indexing (no rounding, no max/min builtins).

    Parameters
    ----------
    log_p : float
        log10 of pressure, already clamped to grid bounds.
    log_t : float
        log10 of temperature, already clamped to valid range.
    grid : numpy.ndarray
        2D array of values, shape (n_p, n_t).
    cached : dict
        Cache entry with grid metadata.

    Returns
    -------
    float
        Interpolated value. NaN if any corner is NaN.
    """
    n_p_m2 = cached['n_p'] - 2
    n_t_m2 = cached['n_t'] - 2

    if n_p_m2 < 0 or n_t_m2 < 0:
        return grid[0, 0]

    # O(1) lower-bound index via floor division
    fp = (log_p - cached['logp_min']) / cached['dlog_p']
    ft = (log_t - cached['logt_min']) / cached['dlog_t']

    ip = int(fp)
    it = int(ft)

    # Clamp to valid range without max/min builtins
    if ip < 0:
        ip = 0
    elif ip > n_p_m2:
        ip = n_p_m2
    if it < 0:
        it = 0
    elif it > n_t_m2:
        it = n_t_m2

    # Fractional position within cell
    dp = fp - ip
    dt = ft - it
    if dp < 0.0:
        dp = 0.0
    elif dp > 1.0:
        dp = 1.0
    if dt < 0.0:
        dt = 0.0
    elif dt > 1.0:
        dt = 1.0

    # Bilinear blend
    omdp = 1.0 - dp
    omdt = 1.0 - dt
    return (
        grid[ip, it] * omdp * omdt
        + grid[ip, it + 1] * omdp * dt
        + grid[ip + 1, it] * dp * omdt
        + grid[ip + 1, it + 1] * dp * dt
    )

_get_paleos_nabla_ad(pressure, temperature, material_dict, phase, interpolation_functions)

Look up nabla_ad from a PALEOS cache entry.

Parameters:

Name Type Description Default
pressure float

Pressure in Pa.

required
temperature float

Temperature in K.

required
material_dict dict

Material properties dict (e.g. material_properties_iron_PALEOS_silicate_planets).

required
phase str

'solid_mantle' or 'melted_mantle'.

required
interpolation_functions dict

Shared interpolation cache.

required

Returns:

Type Description
float or None

Dimensionless adiabatic gradient nabla_ad, or None if lookup fails.

Source code in src/zalmoxis/eos/tdep.py
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def _get_paleos_nabla_ad(pressure, temperature, material_dict, phase, interpolation_functions):
    """Look up nabla_ad from a PALEOS cache entry.

    Parameters
    ----------
    pressure : float
        Pressure in Pa.
    temperature : float
        Temperature in K.
    material_dict : dict
        Material properties dict (e.g. ``material_properties_iron_PALEOS_silicate_planets``).
    phase : str
        ``'solid_mantle'`` or ``'melted_mantle'``.
    interpolation_functions : dict
        Shared interpolation cache.

    Returns
    -------
    float or None
        Dimensionless adiabatic gradient nabla_ad, or None if lookup fails.
    """
    props = material_dict[phase]
    eos_file = props['eos_file']

    # Ensure the PALEOS table is loaded into the cache
    if eos_file not in interpolation_functions:
        interpolation_functions[eos_file] = load_paleos_table(eos_file)

    cached = interpolation_functions[eos_file]
    p_min, p_max = cached['p_min'], cached['p_max']

    # Clamp pressure to global bounds
    p_clamped = np.clip(pressure, p_min, p_max)
    log_p = np.log10(p_clamped)
    log_t = np.log10(max(temperature, 1.0))

    # Per-cell clamping: restrict T to the valid data range at this P
    log_t_clamped, was_clamped = _paleos_clamp_temperature(log_p, log_t, cached)
    if was_clamped and eos_file not in _paleos_clamp_warned:
        _paleos_clamp_warned.add(eos_file)
        logger.warning(
            f'PALEOS per-cell clamping active for nabla_ad in '
            f'{os.path.basename(eos_file)}: '
            f'T={temperature:.0f} K clamped to {10.0**log_t_clamped:.0f} K '
            f'at P={pressure:.2e} Pa.'
        )

    val = float(cached['nabla_ad_interp']((log_p, log_t_clamped)))

    # Nearest-neighbor fallback for ragged boundary
    if not np.isfinite(val):
        val = float(cached['nabla_ad_nn']((log_p, log_t_clamped)))

    if np.isfinite(val):
        return val
    return None

_get_paleos_unified_nabla_ad(pressure, temperature, material_dict, interpolation_functions)

Look up nabla_ad from a unified PALEOS cache entry.

Parameters:

Name Type Description Default
pressure float

Pressure in Pa.

required
temperature float

Temperature in K.

required
material_dict dict

Material properties dict with 'eos_file' key.

required
interpolation_functions dict

Shared interpolation cache.

required

Returns:

Type Description
float or None

Dimensionless adiabatic gradient, or None if lookup fails.

Source code in src/zalmoxis/eos/paleos.py
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def _get_paleos_unified_nabla_ad(pressure, temperature, material_dict, interpolation_functions):
    """Look up nabla_ad from a unified PALEOS cache entry.

    Parameters
    ----------
    pressure : float
        Pressure in Pa.
    temperature : float
        Temperature in K.
    material_dict : dict
        Material properties dict with 'eos_file' key.
    interpolation_functions : dict
        Shared interpolation cache.

    Returns
    -------
    float or None
        Dimensionless adiabatic gradient, or None if lookup fails.
    """
    eos_file = material_dict['eos_file']
    cached = _ensure_unified_cache(eos_file, interpolation_functions)

    p_clamped = np.clip(pressure, cached['p_min'], cached['p_max'])
    log_p = np.log10(p_clamped)
    log_t = np.log10(max(temperature, 1.0))

    log_t_clamped, was_clamped = _paleos_clamp_temperature(log_p, log_t, cached)
    if was_clamped and eos_file not in _paleos_clamp_warned:
        _paleos_clamp_warned.add(eos_file)
        logger.warning(
            f'PALEOS unified per-cell clamping active for nabla_ad in '
            f'{os.path.basename(eos_file)}: '
            f'T={temperature:.0f} K clamped to {10.0**log_t_clamped:.0f} K '
            f'at P={pressure:.2e} Pa.'
        )

    val = _fast_bilinear(log_p, log_t_clamped, cached['nabla_ad_grid'], cached)
    if not np.isfinite(val):
        val = float(cached['nabla_ad_nn']((log_p, log_t_clamped)))

    return val if np.isfinite(val) else None

_paleos_clamp_temperature(log_p, log_t, cached)

Clamp log10(T) to the per-pressure valid range of a PALEOS table.

Uses O(1) index computation on the log-uniform pressure grid instead of np.interp (which does binary search on 1000+ elements). This is called millions of times in the scalar ODE path.

Parameters:

Name Type Description Default
log_p float

log10 of pressure in Pa (already clamped to table bounds).

required
log_t float

log10 of temperature in K.

required
cached dict

PALEOS cache entry.

required

Returns:

Type Description
float

Clamped log10(T).

bool

True if clamping was applied.

Source code in src/zalmoxis/eos/interpolation.py
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def _paleos_clamp_temperature(log_p, log_t, cached):
    """Clamp log10(T) to the per-pressure valid range of a PALEOS table.

    Uses O(1) index computation on the log-uniform pressure grid instead
    of np.interp (which does binary search on 1000+ elements). This is
    called millions of times in the scalar ODE path.

    Parameters
    ----------
    log_p : float
        log10 of pressure in Pa (already clamped to table bounds).
    log_t : float
        log10 of temperature in K.
    cached : dict
        PALEOS cache entry.

    Returns
    -------
    float
        Clamped log10(T).
    bool
        True if clamping was applied.
    """
    lt_min = cached['logt_valid_min']
    lt_max = cached['logt_valid_max']

    # O(1) path for log-uniform grids (has dlog_p metadata)
    if 'dlog_p' in cached:
        fp = (log_p - cached['logp_min']) / cached['dlog_p']
        n_p_m1 = cached['n_p'] - 2
        ip = int(fp)
        if ip < 0:
            ip = 0
        elif ip > n_p_m1:
            ip = n_p_m1
        frac = fp - ip
        if frac < 0.0:
            frac = 0.0
        elif frac > 1.0:
            frac = 1.0
        local_tmin = lt_min[ip] + frac * (lt_min[ip + 1] - lt_min[ip])
        local_tmax = lt_max[ip] + frac * (lt_max[ip + 1] - lt_max[ip])
    else:
        # Fallback for legacy/test cache dicts without grid metadata
        ulp = cached['unique_log_p']
        local_tmin = float(np.interp(log_p, ulp, lt_min))
        local_tmax = float(np.interp(log_p, ulp, lt_max))

    # Guard: NaN bounds near table edges
    if not (local_tmin == local_tmin and local_tmax == local_tmax):  # fast NaN check
        return log_t, False

    if log_t < local_tmin:
        return local_tmin, True
    elif log_t > local_tmax:
        return local_tmax, True
    return log_t, False

calculate_density(pressure, material_dictionaries, layer_eos, temperature, solidus_func, liquidus_func, interpolation_functions=None, mushy_zone_factor=1.0)

Calculate density for a single layer given its EOS identifier.

Parameters:

Name Type Description Default
pressure float

Pressure at which to evaluate the EOS, in Pa.

required
material_dictionaries dict

EOS registry dict keyed by EOS identifier string (from eos_properties.EOS_REGISTRY).

required
layer_eos str

Per-layer EOS identifier, for example "Seager2007:iron", "WolfBower2018:MgSiO3", "PALEOS:iron", or "Analytic:iron".

required
temperature float

Temperature at which to evaluate the EOS, in K.

required
solidus_func callable or None

Interpolation function for the solidus melting curve.

required
liquidus_func callable or None

Interpolation function for the liquidus melting curve.

required
interpolation_functions dict

Cache of interpolation functions used to avoid redundant loading.

None
mushy_zone_factor float

Cryoscopic depression factor for unified PALEOS tables. 1.0 = no mushy zone (sharp boundary from table). Default 1.0.

1.0

Returns:

Type Description
float or None

Density in kg/m^3, or None on failure.

Raises:

Type Description
ValueError

If layer_eos is not recognized.

Source code in src/zalmoxis/eos/dispatch.py
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def calculate_density(
    pressure,
    material_dictionaries,
    layer_eos,
    temperature,
    solidus_func,
    liquidus_func,
    interpolation_functions=None,
    mushy_zone_factor=1.0,
):
    """Calculate density for a single layer given its EOS identifier.

    Parameters
    ----------
    pressure : float
        Pressure at which to evaluate the EOS, in Pa.
    material_dictionaries : dict
        EOS registry dict keyed by EOS identifier string
        (from ``eos_properties.EOS_REGISTRY``).
    layer_eos : str
        Per-layer EOS identifier, for example ``"Seager2007:iron"``,
        ``"WolfBower2018:MgSiO3"``, ``"PALEOS:iron"``, or ``"Analytic:iron"``.
    temperature : float
        Temperature at which to evaluate the EOS, in K.
    solidus_func : callable or None
        Interpolation function for the solidus melting curve.
    liquidus_func : callable or None
        Interpolation function for the liquidus melting curve.
    interpolation_functions : dict, optional
        Cache of interpolation functions used to avoid redundant loading.
    mushy_zone_factor : float, optional
        Cryoscopic depression factor for unified PALEOS tables. 1.0 = no
        mushy zone (sharp boundary from table). Default 1.0.

    Returns
    -------
    float or None
        Density in kg/m^3, or ``None`` on failure.

    Raises
    ------
    ValueError
        If ``layer_eos`` is not recognized.
    """
    if interpolation_functions is None:
        interpolation_functions = {}

    # Analytic EOS: no material dict needed
    if layer_eos.startswith('Analytic:'):
        material_key = layer_eos.split(':', 1)[1]
        return get_analytic_density(pressure, material_key)

    # Vinet (Rose-Vinet) EOS: no material dict needed
    if layer_eos.startswith('Vinet:'):
        material_key = layer_eos.split(':', 1)[1]
        return get_vinet_density(pressure, material_key)

    # Look up material properties from the registry
    mat = material_dictionaries.get(layer_eos)
    if mat is None:
        raise ValueError(f"Unknown layer EOS '{layer_eos}'.")

    # PALEOS-API live tabulation: rewrite the entry in place on first access
    # so the remaining dispatch goes through the normal paleos_unified / paleos
    # code paths. A sticky `_api_resolved` flag short-circuits the full
    # `_is_paleos_api(mat)` dispatch chain on every subsequent RHS call;
    # without it the dispatch check itself dominated the standalone solve
    # (~25M calls per main(), ~6 % of self time in cProfile).
    if '_api_resolved' not in mat:
        if _is_paleos_api(mat):
            from .paleos_api_cache import resolve_registry_entry

            resolve_registry_entry(mat)
        mat['_api_resolved'] = True

    # Unified PALEOS tables (single file per material, all phases included)
    if mat.get('format') == 'paleos_unified':
        return get_paleos_unified_density(
            pressure, temperature, mat, mushy_zone_factor, interpolation_functions
        )

    # T-dependent EOS with separate solid/liquid tables (WB2018, RTPress, PALEOS-2phase)
    if 'melted_mantle' in mat:
        return get_Tdep_density(
            pressure, temperature, mat, solidus_func, liquidus_func, interpolation_functions
        )

    # Seager2007 static EOS (1D P-rho tables)
    # Determine the layer key from the material dict
    for layer_key in ('core', 'mantle', 'ice_layer'):
        if layer_key in mat:
            return get_tabulated_eos(
                pressure, mat, layer_key, interpolation_functions=interpolation_functions
            )

    raise ValueError(f"Cannot determine layer key for EOS '{layer_eos}'.")

calculate_density_batch(pressures, temperatures, material_dictionaries, layer_eos, solidus_func, liquidus_func, interpolation_functions, mushy_zone_factor=1.0)

Vectorized density lookup for a batch of (P, T) points sharing one EOS.

For unified PALEOS tables, uses the vectorized interpolator path. For other EOS types, falls back to scalar calculate_density per point.

Parameters:

Name Type Description Default
pressures ndarray

1D array of pressures in Pa.

required
temperatures ndarray

1D array of temperatures in K.

required
material_dictionaries dict

EOS registry.

required
layer_eos str

EOS identifier string.

required
solidus_func callable or None

Solidus melting curve function.

required
liquidus_func callable or None

Liquidus melting curve function.

required
interpolation_functions dict

Interpolation cache.

required
mushy_zone_factor float

Cryoscopic depression factor.

1.0

Returns:

Type Description
ndarray

1D array of densities in kg/m^3. NaN where lookup fails.

Source code in src/zalmoxis/eos/dispatch.py
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def calculate_density_batch(
    pressures,
    temperatures,
    material_dictionaries,
    layer_eos,
    solidus_func,
    liquidus_func,
    interpolation_functions,
    mushy_zone_factor=1.0,
):
    """Vectorized density lookup for a batch of (P, T) points sharing one EOS.

    For unified PALEOS tables, uses the vectorized interpolator path.
    For other EOS types, falls back to scalar calculate_density per point.

    Parameters
    ----------
    pressures : numpy.ndarray
        1D array of pressures in Pa.
    temperatures : numpy.ndarray
        1D array of temperatures in K.
    material_dictionaries : dict
        EOS registry.
    layer_eos : str
        EOS identifier string.
    solidus_func : callable or None
        Solidus melting curve function.
    liquidus_func : callable or None
        Liquidus melting curve function.
    interpolation_functions : dict
        Interpolation cache.
    mushy_zone_factor : float
        Cryoscopic depression factor.

    Returns
    -------
    numpy.ndarray
        1D array of densities in kg/m^3. NaN where lookup fails.
    """
    if interpolation_functions is None:
        interpolation_functions = {}

    mat = material_dictionaries.get(layer_eos)
    # See calculate_density for the _api_resolved sticky-flag rationale.
    if mat is not None and '_api_resolved' not in mat:
        if _is_paleos_api(mat):
            from .paleos_api_cache import resolve_registry_entry

            resolve_registry_entry(mat)
        mat['_api_resolved'] = True
    if mat is not None and mat.get('format') == 'paleos_unified':
        return get_paleos_unified_density_batch(
            pressures, temperatures, mat, mushy_zone_factor, interpolation_functions
        )

    # Fallback: scalar loop for non-unified EOS types
    n = len(pressures)
    result = np.full(n, np.nan)
    for i in range(n):
        val = calculate_density(
            pressures[i],
            material_dictionaries,
            layer_eos,
            temperatures[i],
            solidus_func,
            liquidus_func,
            interpolation_functions,
            mushy_zone_factor,
        )
        result[i] = val if val is not None else np.nan
    return result

calculate_temperature_profile(radii, temperature_mode, surface_temperature, center_temperature, input_dir, temp_profile_file, cmb_temperature=None)

Return a callable temperature profile for a planetary interior model.

Parameters:

Name Type Description Default
radii array_like

Radial grid of the planet, in m.

required
temperature_mode ('isothermal', 'linear', 'prescribed', 'adiabatic', 'adiabatic_from_cmb')

Temperature profile mode.

  • "isothermal": constant temperature equal to surface_temperature.
  • "linear": linear profile from center_temperature at r = 0 to surface_temperature at the surface.
  • "prescribed": read the temperature profile from a text file.
  • "adiabatic": return a linear profile as an initial guess; the actual adiabat is computed elsewhere in the main iteration loop and is anchored at surface_temperature.
  • "adiabatic_from_cmb": same as "adiabatic" but the actual adiabat (computed elsewhere) is anchored at cmb_temperature at the core-mantle boundary and integrated outward to the surface. The initial guess returned here is still linear, with cmb_temperature used as the deep anchor in place of center_temperature so the first density iteration sees a reasonable mantle T(r).
"isothermal"
surface_temperature float

Temperature at the surface, in K.

required
center_temperature float

Temperature at the center, in K. Used for "linear" and "adiabatic" modes.

required
cmb_temperature float

Temperature at the core-mantle boundary, in K. Required for "adiabatic_from_cmb" mode; ignored otherwise.

None
input_dir str or path - like

Directory containing the prescribed temperature profile file.

required
temp_profile_file str

Name of the file containing the prescribed temperature profile from center to surface. Required when temperature_mode="prescribed".

required

Returns:

Type Description
callable

Function of radius returning temperature in K. The callable accepts a scalar or array-like radius and returns a float or NumPy array.

Raises:

Type Description
ValueError

If temperature_mode="prescribed" and the file does not exist.

ValueError

If the prescribed temperature profile length does not match radii.

ValueError

If temperature_mode is not recognized.

Source code in src/zalmoxis/eos/temperature.py
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def calculate_temperature_profile(
    radii,
    temperature_mode,
    surface_temperature,
    center_temperature,
    input_dir,
    temp_profile_file,
    cmb_temperature=None,
):
    """Return a callable temperature profile for a planetary interior model.

    Parameters
    ----------
    radii : array_like
        Radial grid of the planet, in m.
    temperature_mode : {"isothermal", "linear", "prescribed", "adiabatic", "adiabatic_from_cmb"}
        Temperature profile mode.

        - ``"isothermal"``: constant temperature equal to
          ``surface_temperature``.
        - ``"linear"``: linear profile from ``center_temperature`` at
          ``r = 0`` to ``surface_temperature`` at the surface.
        - ``"prescribed"``: read the temperature profile from a text file.
        - ``"adiabatic"``: return a linear profile as an initial guess; the
          actual adiabat is computed elsewhere in the main iteration loop
          and is anchored at ``surface_temperature``.
        - ``"adiabatic_from_cmb"``: same as ``"adiabatic"`` but the actual
          adiabat (computed elsewhere) is anchored at ``cmb_temperature``
          at the core-mantle boundary and integrated outward to the
          surface. The initial guess returned here is still linear, with
          ``cmb_temperature`` used as the deep anchor in place of
          ``center_temperature`` so the first density iteration sees a
          reasonable mantle T(r).
    surface_temperature : float
        Temperature at the surface, in K.
    center_temperature : float
        Temperature at the center, in K. Used for ``"linear"`` and
        ``"adiabatic"`` modes.
    cmb_temperature : float, optional
        Temperature at the core-mantle boundary, in K. Required for
        ``"adiabatic_from_cmb"`` mode; ignored otherwise.
    input_dir : str or path-like
        Directory containing the prescribed temperature profile file.
    temp_profile_file : str
        Name of the file containing the prescribed temperature profile from
        center to surface. Required when ``temperature_mode="prescribed"``.

    Returns
    -------
    callable
        Function of radius returning temperature in K. The callable accepts a
        scalar or array-like radius and returns a float or NumPy array.

    Raises
    ------
    ValueError
        If ``temperature_mode="prescribed"`` and the file does not exist.
    ValueError
        If the prescribed temperature profile length does not match
        ``radii``.
    ValueError
        If ``temperature_mode`` is not recognized.
    """
    radii = np.array(radii)

    if temperature_mode == 'isothermal':
        return lambda r: np.full_like(r, surface_temperature, dtype=float)

    elif temperature_mode == 'linear':
        return lambda r: (
            surface_temperature
            + (center_temperature - surface_temperature) * (1 - np.array(r) / radii[-1])
        )

    elif temperature_mode == 'prescribed':
        temp_profile_path = os.path.join(input_dir, temp_profile_file)
        if not os.path.exists(temp_profile_path):
            raise ValueError(
                "Temperature profile file must be provided and exist for 'prescribed' temperature mode."
            )
        temp_profile = np.loadtxt(temp_profile_path)
        if len(temp_profile) != len(radii):
            raise ValueError('Temperature profile length does not match radii length.')
        # Vectorized interpolation for arbitrary radius points
        return lambda r: np.interp(np.array(r), radii, temp_profile)

    elif temperature_mode == 'adiabatic':
        # Return linear profile as initial guess for the first outer iteration.
        # The actual adiabat is computed in main() using P(r), g(r) from the solver.
        return lambda r: (
            surface_temperature
            + (center_temperature - surface_temperature) * (1 - np.array(r) / radii[-1])
        )

    elif temperature_mode == 'adiabatic_from_cmb':
        # Initial guess: linear from surface to a deep anchor that uses
        # cmb_temperature when provided (otherwise falls back to
        # center_temperature). The CMB index is unknown at this point in
        # the solve, so anchor at r=0 with the CMB value as a safe
        # over-estimate; the actual upward adiabat from CMB is computed in
        # main() once the converged structure exposes the CMB index.
        deep_anchor = (
            cmb_temperature
            if cmb_temperature is not None and cmb_temperature > 0
            else center_temperature
        )
        return lambda r: (
            surface_temperature
            + (deep_anchor - surface_temperature) * (1 - np.array(r) / radii[-1])
        )

    else:
        raise ValueError(
            f"Unknown temperature mode '{temperature_mode}'. "
            f"Valid options: 'isothermal', 'linear', 'prescribed', 'adiabatic', "
            f"'adiabatic_from_cmb'."
        )

compute_adiabatic_temperature(radii, pressure, mass_enclosed, surface_temperature, cmb_mass, core_mantle_mass, layer_mixtures, material_dictionaries, interpolation_functions=None, solidus_func=None, liquidus_func=None, mushy_zone_factors=None, condensed_rho_min=CONDENSED_RHO_MIN_DEFAULT, condensed_rho_scale=CONDENSED_RHO_SCALE_DEFAULT, binodal_T_scale=50.0, anchor='surface', cmb_temperature=None)

Compute an adiabatic temperature profile using native EOS gradient tables.

Supports single-material and multi-material (volume-additive) layers. For multi-material layers, nabla_ad is mass-fraction-weighted across components.

Parameters:

Name Type Description Default
radii ndarray

Radial grid in ascending order from center to surface, in m.

required
pressure ndarray

Pressure at each radius, in Pa.

required
mass_enclosed ndarray

Enclosed mass at each radius, in kg.

required
surface_temperature float

Temperature at the surface, in K. Used as the anchor when anchor='surface'; carried through as-is for the core when anchor='cmb' (no integration is done below the CMB).

required
cmb_mass float

Core-mantle boundary mass, in kg.

required
core_mantle_mass float

Total core-plus-mantle mass, in kg.

required
layer_mixtures dict

Per-layer LayerMixture objects.

required
material_dictionaries dict

EOS registry dict keyed by EOS identifier string.

required
interpolation_functions dict

Cache of interpolation functions used to avoid redundant loading.

None
solidus_func callable

Interpolation function for the solidus melting curve.

None
liquidus_func callable

Interpolation function for the liquidus melting curve.

None
mushy_zone_factors dict or float or None

Per-EOS mushy zone factors. Dict keyed by EOS name, a single float (applied to all), or None (default 1.0 for all).

None
condensed_rho_min float

Sigmoid center for phase-aware suppression (kg/m^3). Default 322.

CONDENSED_RHO_MIN_DEFAULT
condensed_rho_scale float

Sigmoid width for phase-aware suppression (kg/m^3). Default 50.

CONDENSED_RHO_SCALE_DEFAULT
binodal_T_scale float

Binodal sigmoid width in K for H2 miscibility suppression. Default 50.

50.0
anchor ('surface', 'cmb')

Where the adiabat is anchored. 'surface' (default) anchors T[n-1] = surface_temperature and integrates inward to the center, the original behaviour. 'cmb' anchors T[i_cmb] = cmb_temperature at the first mantle shell and integrates outward to the surface (mantle only); shells below the CMB carry the surface anchor through, since the core adiabat is decoupled and the energetics solver computes T_core independently.

'surface'
cmb_temperature float

Temperature at the core-mantle boundary, in K. Required when anchor='cmb'.

None

Returns:

Type Description
ndarray

Temperature at each radial point, in K.

Source code in src/zalmoxis/eos/temperature.py
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def compute_adiabatic_temperature(
    radii,
    pressure,
    mass_enclosed,
    surface_temperature,
    cmb_mass,
    core_mantle_mass,
    layer_mixtures,
    material_dictionaries,
    interpolation_functions=None,
    solidus_func=None,
    liquidus_func=None,
    mushy_zone_factors=None,
    condensed_rho_min=CONDENSED_RHO_MIN_DEFAULT,
    condensed_rho_scale=CONDENSED_RHO_SCALE_DEFAULT,
    binodal_T_scale=50.0,
    anchor='surface',
    cmb_temperature=None,
):
    """Compute an adiabatic temperature profile using native EOS gradient tables.

    Supports single-material and multi-material (volume-additive) layers.
    For multi-material layers, nabla_ad is mass-fraction-weighted across
    components.

    Parameters
    ----------
    radii : numpy.ndarray
        Radial grid in ascending order from center to surface, in m.
    pressure : numpy.ndarray
        Pressure at each radius, in Pa.
    mass_enclosed : numpy.ndarray
        Enclosed mass at each radius, in kg.
    surface_temperature : float
        Temperature at the surface, in K. Used as the anchor when
        ``anchor='surface'``; carried through as-is for the core when
        ``anchor='cmb'`` (no integration is done below the CMB).
    cmb_mass : float
        Core-mantle boundary mass, in kg.
    core_mantle_mass : float
        Total core-plus-mantle mass, in kg.
    layer_mixtures : dict
        Per-layer LayerMixture objects.
    material_dictionaries : dict
        EOS registry dict keyed by EOS identifier string.
    interpolation_functions : dict, optional
        Cache of interpolation functions used to avoid redundant loading.
    solidus_func : callable, optional
        Interpolation function for the solidus melting curve.
    liquidus_func : callable, optional
        Interpolation function for the liquidus melting curve.
    mushy_zone_factors : dict or float or None, optional
        Per-EOS mushy zone factors. Dict keyed by EOS name, a single
        float (applied to all), or None (default 1.0 for all).
    condensed_rho_min : float, optional
        Sigmoid center for phase-aware suppression (kg/m^3). Default 322.
    condensed_rho_scale : float, optional
        Sigmoid width for phase-aware suppression (kg/m^3). Default 50.
    binodal_T_scale : float, optional
        Binodal sigmoid width in K for H2 miscibility suppression.
        Default 50.
    anchor : {'surface', 'cmb'}, optional
        Where the adiabat is anchored. ``'surface'`` (default) anchors
        ``T[n-1] = surface_temperature`` and integrates inward to the
        center, the original behaviour. ``'cmb'`` anchors
        ``T[i_cmb] = cmb_temperature`` at the first mantle shell and
        integrates outward to the surface (mantle only); shells below
        the CMB carry the surface anchor through, since the core
        adiabat is decoupled and the energetics solver computes T_core
        independently.
    cmb_temperature : float, optional
        Temperature at the core-mantle boundary, in K. Required when
        ``anchor='cmb'``.

    Returns
    -------
    numpy.ndarray
        Temperature at each radial point, in K.
    """
    from ..mixing import get_mixed_nabla_ad
    from ..structure_model import get_layer_mixture

    if interpolation_functions is None:
        interpolation_functions = {}

    from ..mixing import any_component_is_tdep

    if not any_component_is_tdep(layer_mixtures):
        raise ValueError(
            'Adiabatic temperature mode requires at least one T-dependent EOS '
            'layer, but none found. '
            "Use 'linear' or 'isothermal' instead."
        )

    n = len(radii)
    T = np.zeros(n)

    if anchor == 'cmb':
        if cmb_temperature is None or cmb_temperature <= 0:
            raise ValueError(
                f"anchor='cmb' requires a positive cmb_temperature, got {cmb_temperature}."
            )

        # Find the first mantle shell (index where mass_enclosed >= cmb_mass).
        cmb_index = int(np.searchsorted(mass_enclosed, cmb_mass))
        cmb_index = max(1, min(cmb_index, n - 1))

        # Carry the surface anchor through the core (no integration);
        # the energetics solver handles T_core via core_heatcap and the
        # Bower+2018 adiabatic ratio. Anchor the mantle at CMB.
        T[:cmb_index] = surface_temperature
        T[cmb_index] = cmb_temperature

        # Integrate upward from CMB to surface (i = cmb_index .. n-1).
        for i in range(cmb_index + 1, n):
            mixture = get_layer_mixture(
                mass_enclosed[i],
                cmb_mass,
                core_mantle_mass,
                layer_mixtures,
            )

            if not mixture.has_tdep():
                T[i] = T[i - 1]
                continue

            P_eval = pressure[i - 1]
            T_eval = T[i - 1]
            dP = pressure[i] - pressure[i - 1]  # negative going outward

            if P_eval < 1e5 or pressure[i] < 1e5:
                T[i] = T[i - 1]
                continue

            nabla = get_mixed_nabla_ad(
                P_eval,
                T_eval,
                mixture,
                material_dictionaries,
                interpolation_functions,
                solidus_func,
                liquidus_func,
                mushy_zone_factors,
                condensed_rho_min,
                condensed_rho_scale,
                binodal_T_scale,
            )

            if nabla is not None and nabla > 0 and P_eval > 0 and T_eval > 0 and dP < 0:
                dtdp = nabla * T_eval / P_eval
                T_new = T_eval + dtdp * dP  # dP<0 => T cools outward
                T[i] = max(min(T_new, 100000.0), 100.0)
            else:
                T[i] = T_eval

        return T

    # anchor == 'surface' (original behaviour): integrate inward from
    # T[n-1] = surface_temperature to the center.
    T[n - 1] = surface_temperature

    for i in range(n - 2, -1, -1):
        mixture = get_layer_mixture(
            mass_enclosed[i],
            cmb_mass,
            core_mantle_mass,
            layer_mixtures,
        )

        if not mixture.has_tdep():
            T[i] = T[i + 1]
            continue

        P_eval = pressure[i + 1]
        T_eval = T[i + 1]
        dP = pressure[i] - pressure[i + 1]

        # Skip at very low P to prevent T/P divergence
        if P_eval < 1e5 or pressure[i] < 1e5:
            T[i] = T[i + 1]
            continue

        # Get nabla_ad (handles single and multi-component mixtures)
        nabla = get_mixed_nabla_ad(
            P_eval,
            T_eval,
            mixture,
            material_dictionaries,
            interpolation_functions,
            solidus_func,
            liquidus_func,
            mushy_zone_factors,
            condensed_rho_min,
            condensed_rho_scale,
            binodal_T_scale,
        )

        if nabla is not None and nabla > 0 and P_eval > 0 and T_eval > 0 and dP > 0:
            dtdp = nabla * T_eval / P_eval
            T_new = T_eval + dtdp * dP
            # Cap temperature to the PALEOS table maximum (100,000 K).
            # Without this cap, numerical noise at low P or in mixed
            # compositions can cause runaway T during the adiabat
            # integration, which then pollutes the T(P) interpolator
            # and prevents the Brent solver from bracketing.
            T[i] = min(T_new, 100000.0)
        else:
            T[i] = T_eval

    return T

create_pressure_density_files(outer_iter, inner_iter, pressure_iter, radii, pressure, density)

Append pressure and density profiles to output files for a given iteration.

Parameters:

Name Type Description Default
outer_iter int

Current outer iteration index.

required
inner_iter int

Current inner iteration index.

required
pressure_iter int

Current pressure iteration index.

required
radii ndarray

Radial positions, in m.

required
pressure ndarray

Pressure values corresponding to radii, in Pa.

required
density ndarray

Density values corresponding to radii, in kg/m^3.

required

Returns:

Type Description
None
Source code in src/zalmoxis/eos/output.py
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def create_pressure_density_files(
    outer_iter, inner_iter, pressure_iter, radii, pressure, density
):
    """Append pressure and density profiles to output files for a given iteration.

    Parameters
    ----------
    outer_iter : int
        Current outer iteration index.
    inner_iter : int
        Current inner iteration index.
    pressure_iter : int
        Current pressure iteration index.
    radii : numpy.ndarray
        Radial positions, in m.
    pressure : numpy.ndarray
        Pressure values corresponding to ``radii``, in Pa.
    density : numpy.ndarray
        Density values corresponding to ``radii``, in kg/m^3.

    Returns
    -------
    None
    """

    output_dir = os.path.join(get_zalmoxis_root(), 'output')
    os.makedirs(output_dir, exist_ok=True)
    pressure_file = os.path.join(output_dir, 'pressure_profiles.txt')
    density_file = os.path.join(output_dir, 'density_profiles.txt')

    # Only delete the files once at the beginning of the run
    if outer_iter == 0 and inner_iter == 0 and pressure_iter == 0:
        for file_path in [pressure_file, density_file]:
            if os.path.exists(file_path):
                os.remove(file_path)

    # Append current iteration's pressure profile to file
    with open(pressure_file, 'a') as f:
        f.write(f'# Pressure iteration {pressure_iter}\n')
        np.savetxt(f, np.column_stack((radii, pressure)), header='radius pressure', comments='')
        f.write('\n')

    # Append current iteration's density profile to file
    with open(density_file, 'a') as f:
        f.write(f'# Pressure iteration {pressure_iter}\n')
        np.savetxt(f, np.column_stack((radii, density)), header='radius density', comments='')
        f.write('\n')

get_Tdep_density(pressure, temperature, material_properties_iron_Tdep_silicate_planets, solidus_func, liquidus_func, interpolation_functions=None)

Compute mantle density for a temperature-dependent EOS with phase changes.

Parameters:

Name Type Description Default
pressure float

Pressure at which to evaluate the EOS, in Pa.

required
temperature float

Temperature at which to evaluate the EOS, in K.

required
material_properties_iron_Tdep_silicate_planets dict

Dictionary containing temperature-dependent material properties for the MgSiO3 EOS.

required
solidus_func callable

Interpolation function for the solidus melting curve.

required
liquidus_func callable

Interpolation function for the liquidus melting curve.

required
interpolation_functions dict

Cache of interpolation functions used to avoid redundant loading of EOS tables.

None

Returns:

Type Description
float or None

Density in kg/m^3. Returns None if the density cannot be evaluated.

Raises:

Type Description
ValueError

If solidus_func or liquidus_func is not provided.

Notes

The mantle phase is determined by comparing the input temperature to the solidus and liquidus temperatures at the given pressure.

In the mixed-phase region, the density is computed using linear melt fraction and volume additivity.

Source code in src/zalmoxis/eos/tdep.py
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def get_Tdep_density(
    pressure,
    temperature,
    material_properties_iron_Tdep_silicate_planets,
    solidus_func,
    liquidus_func,
    interpolation_functions=None,
):
    """Compute mantle density for a temperature-dependent EOS with phase changes.

    Parameters
    ----------
    pressure : float
        Pressure at which to evaluate the EOS, in Pa.
    temperature : float
        Temperature at which to evaluate the EOS, in K.
    material_properties_iron_Tdep_silicate_planets : dict
        Dictionary containing temperature-dependent material properties for
        the MgSiO3 EOS.
    solidus_func : callable
        Interpolation function for the solidus melting curve.
    liquidus_func : callable
        Interpolation function for the liquidus melting curve.
    interpolation_functions : dict, optional
        Cache of interpolation functions used to avoid redundant loading of
        EOS tables.

    Returns
    -------
    float or None
        Density in kg/m^3. Returns ``None`` if the density cannot be evaluated.

    Raises
    ------
    ValueError
        If ``solidus_func`` or ``liquidus_func`` is not provided.

    Notes
    -----
    The mantle phase is determined by comparing the input temperature to the
    solidus and liquidus temperatures at the given pressure.

    In the mixed-phase region, the density is computed using linear melt
    fraction and volume additivity.
    """

    if interpolation_functions is None:
        interpolation_functions = {}

    if solidus_func is None or liquidus_func is None:
        raise ValueError(
            'solidus_func and liquidus_func must be provided for WolfBower2018:MgSiO3 EOS.'
        )

    T_sol = solidus_func(pressure)
    T_liq = liquidus_func(pressure)

    # Pressure outside melting curve range -- default to solid phase
    if np.isnan(T_sol) or np.isnan(T_liq):
        logger.debug(
            f'Melting curve undefined at P={pressure:.2e} Pa. Defaulting to solid phase.'
        )
        return get_tabulated_eos(
            pressure,
            material_properties_iron_Tdep_silicate_planets,
            'solid_mantle',
            temperature,
            interpolation_functions,
        )

    if temperature <= T_sol:
        # Solid phase
        rho = get_tabulated_eos(
            pressure,
            material_properties_iron_Tdep_silicate_planets,
            'solid_mantle',
            temperature,
            interpolation_functions,
        )
        return rho

    elif temperature >= T_liq:
        # Liquid phase
        rho = get_tabulated_eos(
            pressure,
            material_properties_iron_Tdep_silicate_planets,
            'melted_mantle',
            temperature,
            interpolation_functions,
        )
        return rho

    else:
        # Mixed phase: linear melt fraction between solidus and liquidus.
        # Guard against degenerate melting curves where T_liq == T_sol.
        if T_liq <= T_sol:
            return get_tabulated_eos(
                pressure,
                material_properties_iron_Tdep_silicate_planets,
                'melted_mantle',
                temperature,
                interpolation_functions,
            )
        # Smoothstep ramp s = x*x*(3 - 2*x) replaces the linear melt
        # fraction so d(1/rho)/dT vanishes at T=T_sol and T=T_liq,
        # eliminating the lever-rule kink that drives inner Picard
        # plateau on hot mushy profiles. Midpoint s(0.5)=0.5 = linear,
        # so the in-mushy density profile is preserved away from the
        # boundaries. Mirror change in jax_eos/tdep.py for parity.
        frac_melt_raw = (temperature - T_sol) / (T_liq - T_sol)
        x = max(0.0, min(1.0, frac_melt_raw))
        frac_melt = x * x * (3.0 - 2.0 * x)
        rho_solid = get_tabulated_eos(
            pressure,
            material_properties_iron_Tdep_silicate_planets,
            'solid_mantle',
            temperature,
            interpolation_functions,
        )
        rho_liquid = get_tabulated_eos(
            pressure,
            material_properties_iron_Tdep_silicate_planets,
            'melted_mantle',
            temperature,
            interpolation_functions,
        )
        # Guard against out-of-bounds pressure returning None
        if rho_solid is None or rho_liquid is None:
            return None
        # Calculate mixed density by volume additivity
        specific_volume_mixed = frac_melt * (1 / rho_liquid) + (1 - frac_melt) * (1 / rho_solid)
        rho_mixed = 1 / specific_volume_mixed
        return rho_mixed

get_Tdep_material(pressure, temperature, solidus_func, liquidus_func)

Determine the mantle phase for a temperature-dependent EOS.

Parameters:

Name Type Description Default
pressure float or array_like

Pressure in Pa. May be a scalar or an array.

required
temperature float or array_like

Temperature in K. May be a scalar or an array.

required
solidus_func callable

Interpolation function for the solidus melting curve.

required
liquidus_func callable

Interpolation function for the liquidus melting curve.

required

Returns:

Type Description
str or ndarray

Material phase label(s). Possible values are "solid_mantle", "mixed_mantle", and "melted_mantle". Returns a string for scalar inputs and a NumPy array of strings for array inputs.

Source code in src/zalmoxis/eos/tdep.py
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def get_Tdep_material(pressure, temperature, solidus_func, liquidus_func):
    """Determine the mantle phase for a temperature-dependent EOS.

    Parameters
    ----------
    pressure : float or array_like
        Pressure in Pa. May be a scalar or an array.
    temperature : float or array_like
        Temperature in K. May be a scalar or an array.
    solidus_func : callable
        Interpolation function for the solidus melting curve.
    liquidus_func : callable
        Interpolation function for the liquidus melting curve.

    Returns
    -------
    str or numpy.ndarray
        Material phase label(s). Possible values are ``"solid_mantle"``,
        ``"mixed_mantle"``, and ``"melted_mantle"``. Returns a string for
        scalar inputs and a NumPy array of strings for array inputs.
    """

    # Define per-point evaluation
    def evaluate_phase(P, T):
        T_sol = solidus_func(P)
        T_liq = liquidus_func(P)
        # Guard against degenerate melting curves where T_liq == T_sol
        if T_liq <= T_sol:
            return 'melted_mantle' if T >= T_sol else 'solid_mantle'
        frac_melt = (T - T_sol) / (T_liq - T_sol)
        if frac_melt < 0:
            return 'solid_mantle'
        elif frac_melt <= 1.0:
            return 'mixed_mantle'
        else:
            return 'melted_mantle'

    # Vectorize function for array support
    vectorized_eval = np.vectorize(evaluate_phase, otypes=[str])

    # Apply depending on input type
    if np.isscalar(pressure) and np.isscalar(temperature):
        return evaluate_phase(pressure, temperature)
    else:
        return vectorized_eval(pressure, temperature)

get_paleos_unified_density(pressure, temperature, material_dict, mushy_zone_factor, interpolation_functions)

Look up density from a unified PALEOS table.

When mushy_zone_factor == 1.0 (no mushy zone), the density is read directly from the table (the stable phase at each (P, T) is already encoded). When mushy_zone_factor < 1.0, a synthetic solidus is derived as T_sol = T_liq * mushy_zone_factor and the density in the mushy zone is volume-averaged between the solid-side and liquid-side table values.

Parameters:

Name Type Description Default
pressure float

Pressure in Pa.

required
temperature float

Temperature in K.

required
material_dict dict

Material properties dict with 'eos_file' and 'format' keys.

required
mushy_zone_factor float

Cryoscopic depression factor. 1.0 = no mushy zone (sharp boundary). < 1.0 = solidus at this fraction of the extracted liquidus.

required
interpolation_functions dict

Shared interpolation cache.

required

Returns:

Type Description
float or None

Density in kg/m^3, or None on failure.

Source code in src/zalmoxis/eos/paleos.py
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def get_paleos_unified_density(
    pressure, temperature, material_dict, mushy_zone_factor, interpolation_functions
):
    """Look up density from a unified PALEOS table.

    When ``mushy_zone_factor == 1.0`` (no mushy zone), the density is read
    directly from the table (the stable phase at each (P, T) is already
    encoded). When ``mushy_zone_factor < 1.0``, a synthetic solidus is
    derived as ``T_sol = T_liq * mushy_zone_factor`` and the density in the
    mushy zone is volume-averaged between the solid-side and liquid-side
    table values.

    Parameters
    ----------
    pressure : float
        Pressure in Pa.
    temperature : float
        Temperature in K.
    material_dict : dict
        Material properties dict with 'eos_file' and 'format' keys.
    mushy_zone_factor : float
        Cryoscopic depression factor. 1.0 = no mushy zone (sharp boundary).
        < 1.0 = solidus at this fraction of the extracted liquidus.
    interpolation_functions : dict
        Shared interpolation cache.

    Returns
    -------
    float or None
        Density in kg/m^3, or None on failure.
    """
    eos_file = material_dict['eos_file']
    try:
        cached = _ensure_unified_cache(eos_file, interpolation_functions)

        p_min, p_max = cached['p_min'], cached['p_max']
        if pressure < p_min:
            pressure = p_min
        elif pressure > p_max:
            pressure = p_max

        # W5: math.log10 for scalar input avoids ~1 us/call of numpy-dispatch
        # overhead vs np.log10. Same IEEE-754 result for a Python float input
        # (both ultimately call the same libc log10).
        log_p = math.log10(pressure)
        log_t = math.log10(temperature if temperature > 1.0 else 1.0)

        # Per-cell clamping
        log_t_clamped, was_clamped = _paleos_clamp_temperature(log_p, log_t, cached)
        if was_clamped and eos_file not in _paleos_clamp_warned:
            _paleos_clamp_warned.add(eos_file)
            logger.warning(
                f'PALEOS unified per-cell clamping active for '
                f'{os.path.basename(eos_file)}: '
                f'T={temperature:.0f} K clamped to {10.0**log_t_clamped:.0f} K '
                f'at P={pressure:.2e} Pa.'
            )

        if mushy_zone_factor >= 1.0 or len(cached['liquidus_log_p']) == 0:
            # Direct lookup: no mushy zone (fast bilinear path)
            density = _fast_bilinear(log_p, log_t_clamped, cached['density_grid'], cached)
            if density != density:  # fast NaN check (NaN != NaN)
                density = float(cached['density_nn']((log_p, log_t_clamped)))
            return density if density == density else None

        # Mushy zone: interpolate liquidus T at this P.
        # If query pressure is outside the liquidus coverage (e.g. at
        # pressures where no liquid phase exists), fall back to direct lookup.
        liq_lp = cached['liquidus_log_p']
        if log_p < liq_lp[0] or log_p > liq_lp[-1]:
            density = _fast_bilinear(log_p, log_t_clamped, cached['density_grid'], cached)
            if not np.isfinite(density):
                density = float(cached['density_nn']((log_p, log_t_clamped)))
            return density if np.isfinite(density) else None

        # PALEOS's own melting curve at this pressure
        log_t_melt = float(np.interp(log_p, liq_lp, cached['liquidus_log_t']))
        T_melt = 10.0**log_t_melt

        # Derive mushy zone boundaries (currently from PALEOS liquidus,
        # but may come from external melting curves in future).
        T_liq = T_melt
        T_sol = T_liq * mushy_zone_factor

        # Clamp endpoints against PALEOS's internal phase boundary so that
        # solid-side queries never land on the liquid side and vice versa.
        # The guard offset (_DT_PHASE_GUARD) always shifts T_liq up and may
        # shift T_sol down; only warn when the clamp corrects a genuine
        # cross-boundary incursion (T_sol above T_melt or T_liq below it).
        sol_crossed = T_sol > T_melt
        liq_crossed = T_liq < T_melt
        T_sol = min(T_sol, T_melt - _DT_PHASE_GUARD)
        T_liq = max(T_liq, T_melt + _DT_PHASE_GUARD)

        if sol_crossed or liq_crossed:
            if eos_file not in _paleos_phase_guard_warned:
                _paleos_phase_guard_warned.add(eos_file)
                logger.warning(
                    'Mushy zone endpoints crossed PALEOS melting curve '
                    'for %s at P=%.2e Pa (T_melt=%.1f K): '
                    'T_sol=%.1f K %s, T_liq=%.1f K %s. '
                    'Clamped to safe side.',
                    os.path.basename(eos_file),
                    pressure,
                    T_melt,
                    T_sol,
                    '(was above T_melt)' if sol_crossed else '(ok)',
                    T_liq,
                    '(was below T_melt)' if liq_crossed else '(ok)',
                )
        log_t_sol = math.log10(max(T_sol, 1.0))
        log_t_liq = math.log10(T_liq)

        if temperature >= T_liq:
            # Above liquidus: direct lookup
            density = _fast_bilinear(log_p, log_t_clamped, cached['density_grid'], cached)
            if not np.isfinite(density):
                density = float(cached['density_nn']((log_p, log_t_clamped)))
            return density if np.isfinite(density) else None

        if temperature <= T_sol:
            # Below solidus: direct lookup
            density = _fast_bilinear(log_p, log_t_clamped, cached['density_grid'], cached)
            if not np.isfinite(density):
                density = float(cached['density_nn']((log_p, log_t_clamped)))
            return density if np.isfinite(density) else None

        # In mushy zone: volume-average between solid-side and liquid-side
        phi = (temperature - T_sol) / (T_liq - T_sol)

        # Compute per-P clamp bounds ONCE (inline) rather than calling
        # _paleos_clamp_temperature twice (once for T_sol, once for T_liq) —
        # both clamps share the same log_p, so ip/frac/local_tmin/local_tmax
        # are identical. This saves 2 function calls + dict-lookups per
        # mushy-zone RHS call. Math is identical to _paleos_clamp_temperature;
        # output bit-matches.
        _lt_min = cached['logt_valid_min']
        _lt_max = cached['logt_valid_max']
        if 'dlog_p' in cached:
            _fp = (log_p - cached['logp_min']) / cached['dlog_p']
            _n_p_m1 = cached['n_p'] - 2
            _ip = int(_fp)
            if _ip < 0:  # pragma: no cover - log_p clamped earlier; defensive
                _ip = 0
            elif _ip > _n_p_m1:  # pragma: no cover - log_p clamped earlier; defensive
                _ip = _n_p_m1
            _frac = _fp - _ip
            if (
                _frac < 0.0
            ):  # pragma: no cover - frac is non-negative by construction; defensive
                _frac = 0.0
            elif _frac > 1.0:  # pragma: no cover - frac is bounded by construction; defensive
                _frac = 1.0
            _local_tmin = _lt_min[_ip] + _frac * (_lt_min[_ip + 1] - _lt_min[_ip])
            _local_tmax = _lt_max[_ip] + _frac * (_lt_max[_ip + 1] - _lt_max[_ip])
        else:
            _ulp = cached['unique_log_p']
            _local_tmin = float(np.interp(log_p, _ulp, _lt_min))
            _local_tmax = float(np.interp(log_p, _ulp, _lt_max))

        # NaN-bound fallback matches _paleos_clamp_temperature's contract:
        # if bounds are NaN near table edges, return the input log_t unclamped.
        if _local_tmin == _local_tmin and _local_tmax == _local_tmax:
            if log_t_sol < _local_tmin:
                log_t_sol_c = _local_tmin
            elif log_t_sol > _local_tmax:
                log_t_sol_c = _local_tmax
            else:
                log_t_sol_c = log_t_sol
            if log_t_liq < _local_tmin:
                log_t_liq_c = _local_tmin
            elif log_t_liq > _local_tmax:
                log_t_liq_c = _local_tmax
            else:
                log_t_liq_c = log_t_liq
        else:
            log_t_sol_c = log_t_sol
            log_t_liq_c = log_t_liq

        # Solid-side: density at T_sol
        rho_sol = _fast_bilinear(log_p, log_t_sol_c, cached['density_grid'], cached)
        if not np.isfinite(rho_sol):
            rho_sol = float(cached['density_nn']((log_p, log_t_sol_c)))

        # Liquid-side: density at T_liq
        rho_liq = _fast_bilinear(log_p, log_t_liq_c, cached['density_grid'], cached)
        if not np.isfinite(rho_liq):
            rho_liq = float(cached['density_nn']((log_p, log_t_liq_c)))

        if not (np.isfinite(rho_sol) and np.isfinite(rho_liq)):
            return None

        # Volume additivity
        specific_volume = phi * (1.0 / rho_liq) + (1.0 - phi) * (1.0 / rho_sol)
        return 1.0 / specific_volume

    except Exception as e:
        logger.error(
            f'Error in PALEOS unified density at P={pressure:.2e} Pa, '
            f'T={temperature:.1f} K: {e}'
        )
        return None

get_paleos_unified_density_batch(pressures, temperatures, material_dict, mushy_zone_factor, interpolation_functions)

Vectorized density lookup from a unified PALEOS table.

Parameters:

Name Type Description Default
pressures ndarray

1D array of pressures in Pa.

required
temperatures ndarray

1D array of temperatures in K.

required
material_dict dict

Material properties dict with 'eos_file' and 'format' keys.

required
mushy_zone_factor float

Cryoscopic depression factor. 1.0 = no mushy zone.

required
interpolation_functions dict

Shared interpolation cache.

required

Returns:

Type Description
ndarray

1D array of densities in kg/m^3. NaN where lookup fails.

Source code in src/zalmoxis/eos/paleos.py
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def get_paleos_unified_density_batch(
    pressures, temperatures, material_dict, mushy_zone_factor, interpolation_functions
):
    """Vectorized density lookup from a unified PALEOS table.

    Parameters
    ----------
    pressures : numpy.ndarray
        1D array of pressures in Pa.
    temperatures : numpy.ndarray
        1D array of temperatures in K.
    material_dict : dict
        Material properties dict with 'eos_file' and 'format' keys.
    mushy_zone_factor : float
        Cryoscopic depression factor. 1.0 = no mushy zone.
    interpolation_functions : dict
        Shared interpolation cache.

    Returns
    -------
    numpy.ndarray
        1D array of densities in kg/m^3. NaN where lookup fails.
    """
    eos_file = material_dict['eos_file']
    cached = _ensure_unified_cache(eos_file, interpolation_functions)

    p_clamped = np.clip(pressures, cached['p_min'], cached['p_max'])
    log_p = np.log10(p_clamped)
    log_t = np.log10(np.maximum(temperatures, 1.0))

    # Per-cell clamping (vectorized)
    ulp = cached['unique_log_p']
    lt_min = cached['logt_valid_min']
    lt_max = cached['logt_valid_max']
    local_tmin = np.interp(log_p, ulp, lt_min)
    local_tmax = np.interp(log_p, ulp, lt_max)

    valid_bounds = np.isfinite(local_tmin) & np.isfinite(local_tmax)
    log_t_clamped = log_t.copy()
    log_t_clamped = np.where(valid_bounds & (log_t < local_tmin), local_tmin, log_t_clamped)
    log_t_clamped = np.where(valid_bounds & (log_t > local_tmax), local_tmax, log_t_clamped)

    if mushy_zone_factor >= 1.0 or len(cached['liquidus_log_p']) == 0:
        # Direct lookup: fast vectorized bilinear interpolation
        result = fast_bilinear_batch(log_p, log_t_clamped, cached['density_grid'], cached)
        # NN fallback for NaN entries
        nan_mask = ~np.isfinite(result)
        if np.any(nan_mask):
            pts_nn = np.column_stack([log_p[nan_mask], log_t_clamped[nan_mask]])
            result[nan_mask] = cached['density_nn'](pts_nn)
        return result

    # Mushy zone path (vectorized).
    # Compute T_melt from the PALEOS analytic melting curve rather than
    # interpolating the extracted liquidus grid. This is faster and avoids
    # branching per-element for the "outside liquidus coverage" case.
    from ..melting_curves import paleos_liquidus

    T_melt = paleos_liquidus(pressures)

    # Derive mushy zone boundaries (currently from PALEOS liquidus,
    # but may come from external melting curves in future).
    T_liq = T_melt.copy()
    T_sol = T_liq * mushy_zone_factor

    # Clamp endpoints against PALEOS's own melting curve
    T_sol = np.minimum(T_sol, T_melt - _DT_PHASE_GUARD)
    T_liq = np.maximum(T_liq, T_melt + _DT_PHASE_GUARD)

    log_t_sol = np.log10(np.maximum(T_sol, 1.0))
    log_t_liq = np.log10(np.maximum(T_liq, 1.0))

    # Classify shells: above liquidus, below solidus, or in mushy zone
    above = temperatures >= T_liq
    below = temperatures <= T_sol
    mushy = ~above & ~below

    # Direct lookup for above-liquidus and below-solidus shells
    result = fast_bilinear_batch(log_p, log_t_clamped, cached['density_grid'], cached)
    nan_mask = ~np.isfinite(result)
    if np.any(nan_mask):
        pts_nn = np.column_stack([log_p[nan_mask], log_t_clamped[nan_mask]])
        result[nan_mask] = cached['density_nn'](pts_nn)

    # Mushy zone shells: volume-average between solid-side and liquid-side
    if np.any(mushy):
        m_idx = np.where(mushy)[0]
        phi = (temperatures[m_idx] - T_sol[m_idx]) / (T_liq[m_idx] - T_sol[m_idx])

        # Solid-side density at T_sol
        log_t_sol_c = log_t_sol[m_idx].copy()
        sol_tmin = np.interp(log_p[m_idx], ulp, lt_min)
        sol_tmax = np.interp(log_p[m_idx], ulp, lt_max)
        sol_valid = np.isfinite(sol_tmin) & np.isfinite(sol_tmax)
        log_t_sol_c = np.where(sol_valid & (log_t_sol_c < sol_tmin), sol_tmin, log_t_sol_c)
        log_t_sol_c = np.where(sol_valid & (log_t_sol_c > sol_tmax), sol_tmax, log_t_sol_c)
        rho_sol = fast_bilinear_batch(log_p[m_idx], log_t_sol_c, cached['density_grid'], cached)
        nn_sol = ~np.isfinite(rho_sol)
        if np.any(nn_sol):
            pts_sol_nn = np.column_stack([log_p[m_idx][nn_sol], log_t_sol_c[nn_sol]])
            rho_sol[nn_sol] = cached['density_nn'](pts_sol_nn)

        # Liquid-side density at T_liq
        log_t_liq_c = log_t_liq[m_idx].copy()
        liq_tmin = np.interp(log_p[m_idx], ulp, lt_min)
        liq_tmax = np.interp(log_p[m_idx], ulp, lt_max)
        liq_valid = np.isfinite(liq_tmin) & np.isfinite(liq_tmax)
        log_t_liq_c = np.where(liq_valid & (log_t_liq_c < liq_tmin), liq_tmin, log_t_liq_c)
        log_t_liq_c = np.where(liq_valid & (log_t_liq_c > liq_tmax), liq_tmax, log_t_liq_c)
        rho_liq = fast_bilinear_batch(log_p[m_idx], log_t_liq_c, cached['density_grid'], cached)
        nn_liq = ~np.isfinite(rho_liq)
        if np.any(nn_liq):
            pts_liq_nn = np.column_stack([log_p[m_idx][nn_liq], log_t_liq_c[nn_liq]])
            rho_liq[nn_liq] = cached['density_nn'](pts_liq_nn)

        # Volume additivity
        both_ok = np.isfinite(rho_sol) & np.isfinite(rho_liq) & (rho_sol > 0) & (rho_liq > 0)
        spec_vol = phi * (1.0 / np.where(both_ok, rho_liq, 1.0)) + (1.0 - phi) * (
            1.0 / np.where(both_ok, rho_sol, 1.0)
        )
        result[m_idx] = np.where(both_ok, 1.0 / spec_vol, np.nan)

    return result

get_solidus_liquidus_functions(solidus_id='Stixrude14-solidus', liquidus_id='Stixrude14-liquidus')

Load solidus and liquidus melting curves by config identifier.

Delegates to :func:zalmoxis.melting_curves.get_solidus_liquidus_functions.

Parameters:

Name Type Description Default
solidus_id str

Solidus curve identifier.

'Stixrude14-solidus'
liquidus_id str

Liquidus curve identifier.

'Stixrude14-liquidus'

Returns:

Type Description
tuple of callable

(solidus_func, liquidus_func)

Source code in src/zalmoxis/eos/tdep.py
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def get_solidus_liquidus_functions(
    solidus_id='Stixrude14-solidus', liquidus_id='Stixrude14-liquidus'
):
    """Load solidus and liquidus melting curves by config identifier.

    Delegates to :func:`zalmoxis.melting_curves.get_solidus_liquidus_functions`.

    Parameters
    ----------
    solidus_id : str
        Solidus curve identifier.
    liquidus_id : str
        Liquidus curve identifier.

    Returns
    -------
    tuple of callable
        ``(solidus_func, liquidus_func)``
    """
    from ..melting_curves import get_solidus_liquidus_functions as _get

    return _get(solidus_id, liquidus_id)

get_tabulated_eos(pressure, material_dictionary, material, temperature=None, interpolation_functions=None)

Retrieve density from tabulated EOS data for a given material.

Parameters:

Name Type Description Default
pressure float

Pressure at which to evaluate the EOS, in Pa.

required
material_dictionary dict

Dictionary containing material properties and EOS file paths.

required
material str

Material type, for example "core", "mantle", "ice_layer", "melted_mantle", or "solid_mantle".

required
temperature float

Temperature at which to evaluate the EOS, in K. Required for temperature-dependent materials such as "melted_mantle" and "solid_mantle".

None
interpolation_functions dict

Cache of interpolation functions used to avoid reloading and rebuilding interpolators for EOS tables.

None

Returns:

Type Description
float or None

Density in kg/m^3 if the interpolation succeeds, otherwise None.

Source code in src/zalmoxis/eos/seager.py
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def get_tabulated_eos(
    pressure, material_dictionary, material, temperature=None, interpolation_functions=None
):
    """Retrieve density from tabulated EOS data for a given material.

    Parameters
    ----------
    pressure : float
        Pressure at which to evaluate the EOS, in Pa.
    material_dictionary : dict
        Dictionary containing material properties and EOS file paths.
    material : str
        Material type, for example ``"core"``, ``"mantle"``,
        ``"ice_layer"``, ``"melted_mantle"``, or ``"solid_mantle"``.
    temperature : float, optional
        Temperature at which to evaluate the EOS, in K. Required for
        temperature-dependent materials such as ``"melted_mantle"`` and
        ``"solid_mantle"``.
    interpolation_functions : dict, optional
        Cache of interpolation functions used to avoid reloading and
        rebuilding interpolators for EOS tables.

    Returns
    -------
    float or None
        Density in kg/m^3 if the interpolation succeeds, otherwise ``None``.
    """
    if interpolation_functions is None:
        interpolation_functions = {}
    props = material_dictionary[material]
    eos_file = props['eos_file']
    is_paleos = props.get('format') == 'paleos'
    try:
        if eos_file not in interpolation_functions:
            if is_paleos:
                # PALEOS 10-column format with log-log grid
                interpolation_functions[eos_file] = load_paleos_table(eos_file)
            elif material == 'melted_mantle' or material == 'solid_mantle':
                # Load P-T-rho file
                data = np.loadtxt(eos_file, delimiter='\t', skiprows=1)
                pressures = data[:, 0]  # in Pa
                temps = data[:, 1]  # in K
                densities = data[:, 2]  # in kg/m^3
                unique_pressures = np.unique(pressures)
                unique_temps = np.unique(temps)

                is_regular = len(data) == len(unique_pressures) * len(unique_temps)

                if is_regular:
                    # Check if pressures and temps are sorted as expected
                    if not (
                        np.all(np.diff(unique_pressures) > 0)
                        and np.all(np.diff(unique_temps) > 0)
                    ):  # pragma: no cover - shipped Seager tables are sorted by construction; defensive
                        raise ValueError(
                            'Pressures or temperatures are not sorted as expected in EOS file.'
                        )

                    # Reshape densities to a 2D grid for interpolation
                    density_grid = densities.reshape(len(unique_pressures), len(unique_temps))

                    # Create a RegularGridInterpolator for rho(P,T)
                    interpolator = RegularGridInterpolator(
                        (unique_pressures, unique_temps),
                        density_grid,
                        bounds_error=False,
                        fill_value=None,
                    )
                    interpolation_functions[eos_file] = {
                        'type': 'regular',
                        'interp': interpolator,
                        'p_min': unique_pressures[0],
                        'p_max': unique_pressures[-1],
                        't_min': unique_temps[0],
                        't_max': unique_temps[-1],
                    }
                else:
                    # Irregular grid (e.g. RTPress100TPa melt table where the
                    # valid T range varies with P). Use scattered-data
                    # interpolation via Delaunay triangulation.
                    logger.info(
                        f'EOS file {eos_file} has irregular grid '
                        f'({len(data)} rows vs {len(unique_pressures)}x{len(unique_temps)} '
                        f'= {len(unique_pressures) * len(unique_temps)} expected). '
                        f'Using LinearNDInterpolator.'
                    )
                    # Work in log-P space for better triangulation of the
                    # logarithmically spaced pressure axis
                    log_pressures = np.log10(pressures)
                    interpolator = LinearNDInterpolator(
                        np.column_stack([log_pressures, temps]),
                        densities,
                    )
                    interpolation_functions[eos_file] = {
                        'type': 'irregular',
                        'interp': interpolator,
                        'p_min': unique_pressures[0],
                        'p_max': unique_pressures[-1],
                        't_min': unique_temps[0],
                        't_max': unique_temps[-1],
                        # Per-pressure T bounds for out-of-domain detection
                        'p_tmax': {p: temps[pressures == p].max() for p in unique_pressures},
                        'unique_pressures': unique_pressures,
                    }
            else:
                # Load rho-P file
                data = np.loadtxt(eos_file, delimiter=',', skiprows=1)
                pressure_data = data[:, 1] * 1e9  # Convert from GPa to Pa
                density_data = data[:, 0] * 1e3  # Convert from g/cm^3 to kg/m^3
                interpolation_functions[eos_file] = {
                    'type': '1d',
                    'interp': interp1d(
                        pressure_data,
                        density_data,
                        bounds_error=False,
                        fill_value='extrapolate',
                    ),
                }

        cached = interpolation_functions[eos_file]  # Retrieve from cache

        # Perform interpolation
        if cached['type'] == 'paleos':
            # PALEOS: interpolate in log10(P)-log10(T) space
            if temperature is None:
                raise ValueError('Temperature must be provided.')
            p_min, p_max = cached['p_min'], cached['p_max']

            # Clamp pressure to global bounds
            if pressure < p_min or pressure > p_max:
                logger.debug(
                    f'PALEOS: Pressure {pressure:.2e} Pa out of bounds '
                    f'[{p_min:.2e}, {p_max:.2e}]. Clamping.'
                )
                pressure = np.clip(pressure, p_min, p_max)

            log_p = np.log10(pressure)
            log_t = np.log10(max(temperature, 1.0))  # guard log10(0)

            # Per-cell clamping: restrict T to the valid data range at this P
            log_t_clamped, was_clamped = _paleos_clamp_temperature(log_p, log_t, cached)
            if was_clamped and eos_file not in _paleos_clamp_warned:
                _paleos_clamp_warned.add(eos_file)
                t_orig = temperature
                t_new = 10.0**log_t_clamped
                logger.warning(
                    f'PALEOS per-cell clamping active for {os.path.basename(eos_file)}: '
                    f'T={t_orig:.0f} K clamped to {t_new:.0f} K at P={pressure:.2e} Pa. '
                    f'The table has no valid data at this (P,T). '
                    f'Density values near the table boundary may be inaccurate.'
                )

            density = _fast_bilinear(log_p, log_t_clamped, cached['density_grid'], cached)

            # Nearest-neighbor fallback: bilinear interpolation returns NaN
            # when a valid cell neighbors a NaN cell near the ragged domain
            # boundary. Fall back to the nearest valid grid cell.
            if not np.isfinite(density):
                density = float(cached['density_nn']((log_p, log_t_clamped)))
        elif material == 'melted_mantle' or material == 'solid_mantle':
            if temperature is None:
                raise ValueError('Temperature must be provided.')

            grid_type = cached['type']
            p_min, p_max = cached['p_min'], cached['p_max']
            t_min, t_max = cached['t_min'], cached['t_max']

            # Global temperature bounds check
            if temperature < t_min or temperature > t_max:
                raise ValueError(
                    f'Temperature {temperature:.2f} K is out of bounds '
                    f'for EOS data [{t_min:.1f}, {t_max:.1f}].'
                )

            # Pressure clamping (both grid types)
            if pressure < p_min or pressure > p_max:
                logger.debug(
                    f'Pressure {pressure:.2e} Pa out of bounds for EOS table '
                    f'[{p_min:.2e}, {p_max:.2e}]. Clamping to boundary.'
                )
                pressure = np.clip(pressure, p_min, p_max)

            if grid_type == 'regular':
                density = cached['interp']((pressure, temperature))
            else:
                up = cached['unique_pressures']
                idx = np.searchsorted(up, pressure, side='right')
                idx = min(idx, len(up) - 1)
                idx_lo = max(0, idx - 1)
                local_tmax_lo = cached['p_tmax'][up[idx_lo]]
                local_tmax_hi = cached['p_tmax'][up[idx]]
                if up[idx] != up[idx_lo]:
                    frac = (pressure - up[idx_lo]) / (up[idx] - up[idx_lo])
                    local_tmax = local_tmax_lo + frac * (local_tmax_hi - local_tmax_lo)
                else:
                    local_tmax = local_tmax_lo

                if temperature > local_tmax:
                    logger.debug(
                        f'Temperature {temperature:.1f} K exceeds local T_max '
                        f'{local_tmax:.1f} K at P={pressure:.2e} Pa. '
                        f'Clamping to boundary.'
                    )
                    temperature = local_tmax

                density = float(cached['interp']([[np.log10(pressure), temperature]])[0])
        else:
            density = cached['interp'](pressure)

        if density is None or not np.isfinite(
            density
        ):  # pragma: no cover - lookup-failed sentinel; defensive
            raise ValueError(
                f'Density calculation failed for {material} at P={pressure:.2e} Pa, T={temperature}.'
            )

        return density

    except (ValueError, OSError) as e:
        logger.error(
            f'Error with tabulated EOS for {material} at P={pressure:.2e} Pa, T={temperature}: {e}'
        )
        return None
    except Exception as e:
        logger.error(
            f'Unexpected error with tabulated EOS for {material} at P={pressure:.2e} Pa, T={temperature}: {e}'
        )
        return None

load_melting_curve(melt_file)

Load a melting curve for MgSiO3 from a text file.

Parameters:

Name Type Description Default
melt_file str or path - like

Path to the melting curve data file. The file is expected to contain two columns: pressure in Pa and temperature in K.

required

Returns:

Type Description
interp1d or None

One-dimensional interpolation function returning temperature as a function of pressure. Returns None if the file cannot be loaded.

Source code in src/zalmoxis/eos/tdep.py
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def load_melting_curve(melt_file):
    """Load a melting curve for MgSiO3 from a text file.

    Parameters
    ----------
    melt_file : str or path-like
        Path to the melting curve data file. The file is expected to contain
        two columns: pressure in Pa and temperature in K.

    Returns
    -------
    scipy.interpolate.interp1d or None
        One-dimensional interpolation function returning temperature as a
        function of pressure. Returns ``None`` if the file cannot be loaded.
    """
    from scipy.interpolate import interp1d

    try:
        data = np.loadtxt(melt_file, comments='#')
        pressures = data[:, 0]  # in Pa
        temperatures = data[:, 1]  # in K
        interp_func = interp1d(
            pressures, temperatures, kind='linear', bounds_error=False, fill_value=np.nan
        )
        return interp_func
    except Exception as e:
        print(f'Error loading melting curve data: {e}')
        return None

load_paleos_table(eos_file)

Load a PALEOS MgSiO3 table and build RegularGridInterpolator objects.

The PALEOS tables have 10 columns (SI units): P, T, rho, u, s, cp, cv, alpha, nabla_ad, phase_id(string). The grid is log-uniform in both P and T with 150 points per decade. Some grid cells are missing (unconverged corners), filled with NaN. A P=0 row may exist and is excluded for log interpolation.

Parameters:

Name Type Description Default
eos_file str

Path to the PALEOS table file.

required

Returns:

Type Description
dict

Cache entry with keys: - 'type': 'paleos' - 'density_interp': RegularGridInterpolator for rho(log10P, log10T) - 'nabla_ad_interp': RegularGridInterpolator for nabla_ad(log10P, log10T) - 'p_min', 'p_max': pressure bounds in Pa - 't_min', 't_max': temperature bounds in K

Source code in src/zalmoxis/eos/interpolation.py
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def load_paleos_table(eos_file):
    """Load a PALEOS MgSiO3 table and build RegularGridInterpolator objects.

    The PALEOS tables have 10 columns (SI units):
    P, T, rho, u, s, cp, cv, alpha, nabla_ad, phase_id(string).
    The grid is log-uniform in both P and T with 150 points per decade.
    Some grid cells are missing (unconverged corners), filled with NaN.
    A P=0 row may exist and is excluded for log interpolation.

    Parameters
    ----------
    eos_file : str
        Path to the PALEOS table file.

    Returns
    -------
    dict
        Cache entry with keys:
        - ``'type'``: ``'paleos'``
        - ``'density_interp'``: RegularGridInterpolator for rho(log10P, log10T)
        - ``'nabla_ad_interp'``: RegularGridInterpolator for nabla_ad(log10P, log10T)
        - ``'p_min'``, ``'p_max'``: pressure bounds in Pa
        - ``'t_min'``, ``'t_max'``: temperature bounds in K
    """
    # Read only numeric columns (0-8), skipping the string phase_id column (9)
    data = np.genfromtxt(eos_file, usecols=range(9), comments='#')

    pressures = data[:, 0]
    temps = data[:, 1]
    densities = data[:, 2]
    nabla_ad = data[:, 8]

    # Filter out P=0 rows (log10(0) is undefined)
    valid = pressures > 0
    pressures = pressures[valid]
    temps = temps[valid]
    densities = densities[valid]
    nabla_ad = nabla_ad[valid]

    # Work in log10 space for the grid axes
    log_p = np.log10(pressures)
    log_t = np.log10(temps)

    unique_log_p = np.unique(log_p)
    unique_log_t = np.unique(log_t)

    n_p = len(unique_log_p)
    n_t = len(unique_log_t)

    # Build 2D grids filled with NaN for missing cells
    density_grid = np.full((n_p, n_t), np.nan)
    nabla_ad_grid = np.full((n_p, n_t), np.nan)

    # Map log_p and log_t values to grid indices
    p_idx_map = {v: i for i, v in enumerate(unique_log_p)}
    t_idx_map = {v: i for i, v in enumerate(unique_log_t)}

    for k in range(len(pressures)):
        ip = p_idx_map[log_p[k]]
        it = t_idx_map[log_t[k]]
        density_grid[ip, it] = densities[k]
        nabla_ad_grid[ip, it] = nabla_ad[k]

    density_interp = RegularGridInterpolator(
        (unique_log_p, unique_log_t),
        density_grid,
        bounds_error=False,
        fill_value=np.nan,
    )
    nabla_ad_interp = RegularGridInterpolator(
        (unique_log_p, unique_log_t),
        nabla_ad_grid,
        bounds_error=False,
        fill_value=np.nan,
    )

    # Per-pressure valid T bounds for per-cell clamping.
    # At each pressure row, find the min and max log10(T) with finite density.
    # This lets us clamp queries into the valid domain when the grid has NaN
    # holes in the corners (e.g. high T at low P in the liquid table).
    logt_valid_min = np.full(n_p, np.nan)
    logt_valid_max = np.full(n_p, np.nan)
    for ip in range(n_p):
        finite_mask = np.isfinite(density_grid[ip, :])
        if finite_mask.any():
            valid_indices = np.where(finite_mask)[0]
            logt_valid_min[ip] = unique_log_t[valid_indices[0]]
            logt_valid_max[ip] = unique_log_t[valid_indices[-1]]

    # Nearest-neighbor fallback interpolators built from valid cells only.
    # Used when bilinear interpolation returns NaN near the ragged domain
    # boundary (a valid cell neighboring a NaN cell poisons bilinear output).
    valid_cells = np.isfinite(density_grid)
    ip_valid, it_valid = np.where(valid_cells)
    coords_valid = np.column_stack([unique_log_p[ip_valid], unique_log_t[it_valid]])

    density_nn = NearestNDInterpolator(coords_valid, density_grid[valid_cells])
    nabla_ad_nn = NearestNDInterpolator(
        coords_valid[np.isfinite(nabla_ad_grid[valid_cells])],
        nabla_ad_grid[valid_cells][np.isfinite(nabla_ad_grid[valid_cells])],
    )

    # Precompute grid spacing for O(1) bilinear interpolation.
    dlog_p = (unique_log_p[-1] - unique_log_p[0]) / (n_p - 1) if n_p > 1 else 1.0
    dlog_t = (unique_log_t[-1] - unique_log_t[0]) / (n_t - 1) if n_t > 1 else 1.0

    return {
        'type': 'paleos',
        'density_interp': density_interp,
        'nabla_ad_interp': nabla_ad_interp,
        'density_nn': density_nn,
        'nabla_ad_nn': nabla_ad_nn,
        'p_min': 10.0 ** unique_log_p[0],
        'p_max': 10.0 ** unique_log_p[-1],
        't_min': 10.0 ** unique_log_t[0],
        't_max': 10.0 ** unique_log_t[-1],
        'unique_log_p': unique_log_p,
        'unique_log_t': unique_log_t,
        'logt_valid_min': logt_valid_min,
        'logt_valid_max': logt_valid_max,
        # Fast bilinear interpolation data
        'density_grid': density_grid,
        'nabla_ad_grid': nabla_ad_grid,
        'logp_min': unique_log_p[0],
        'logp_max': unique_log_p[-1],
        'logt_min': unique_log_t[0],
        'logt_max': unique_log_t[-1],
        'dlog_p': dlog_p,
        'dlog_t': dlog_t,
        'n_p': n_p,
        'n_t': n_t,
    }

load_paleos_unified_table(eos_file)

Load a unified PALEOS table (single file per material) and build interpolators.

The unified tables use the same 10-column format as the 2-phase tables (P, T, rho, u, s, cp, cv, alpha, nabla_ad, phase_id) but contain all stable phases for a material in a single file. The thermodynamically stable phase at each (P, T) is encoded in the phase column.

In addition to density and nabla_ad interpolators, this function extracts the liquidus boundary from the phase column: for each pressure row, it finds the lowest temperature where the phase is 'liquid'.

Parameters:

Name Type Description Default
eos_file str

Path to the unified PALEOS table file.

required

Returns:

Type Description
dict

Cache entry with keys: - 'type': 'paleos_unified' - 'density_interp': RegularGridInterpolator for rho(log10P, log10T) - 'nabla_ad_interp': RegularGridInterpolator for nabla_ad(log10P, log10T) - 'density_nn', 'nabla_ad_nn': NearestNDInterpolator fallbacks - 'p_min', 'p_max': pressure bounds in Pa - 't_min', 't_max': temperature bounds in K - 'unique_log_p': unique log10(P) grid values - 'logt_valid_min', 'logt_valid_max': per-pressure T bounds - 'liquidus_log_p': log10(P) array for the extracted liquidus - 'liquidus_log_t': log10(T_liquidus) array at each pressure - 'phase_grid': 2D string array of phase identifiers

Source code in src/zalmoxis/eos/interpolation.py
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def load_paleos_unified_table(eos_file):
    """Load a unified PALEOS table (single file per material) and build interpolators.

    The unified tables use the same 10-column format as the 2-phase tables
    (P, T, rho, u, s, cp, cv, alpha, nabla_ad, phase_id) but contain all
    stable phases for a material in a single file. The thermodynamically
    stable phase at each (P, T) is encoded in the phase column.

    In addition to density and nabla_ad interpolators, this function
    extracts the liquidus boundary from the phase column: for each pressure
    row, it finds the lowest temperature where the phase is 'liquid'.

    Parameters
    ----------
    eos_file : str
        Path to the unified PALEOS table file.

    Returns
    -------
    dict
        Cache entry with keys:
        - ``'type'``: ``'paleos_unified'``
        - ``'density_interp'``: RegularGridInterpolator for rho(log10P, log10T)
        - ``'nabla_ad_interp'``: RegularGridInterpolator for nabla_ad(log10P, log10T)
        - ``'density_nn'``, ``'nabla_ad_nn'``: NearestNDInterpolator fallbacks
        - ``'p_min'``, ``'p_max'``: pressure bounds in Pa
        - ``'t_min'``, ``'t_max'``: temperature bounds in K
        - ``'unique_log_p'``: unique log10(P) grid values
        - ``'logt_valid_min'``, ``'logt_valid_max'``: per-pressure T bounds
        - ``'liquidus_log_p'``: log10(P) array for the extracted liquidus
        - ``'liquidus_log_t'``: log10(T_liquidus) array at each pressure
        - ``'phase_grid'``: 2D string array of phase identifiers
    """
    # Single-pass read: parse numeric columns and phase string together.
    # Avoids the 2x penalty of calling genfromtxt twice on 50-140 MB files.
    numeric_rows = []
    phase_list = []
    with open(eos_file) as f:
        for line in f:
            line = line.strip()
            if not line or line.startswith('#'):
                continue
            parts = line.split()
            numeric_rows.append([float(x) for x in parts[:9]])
            phase_list.append(parts[9] if len(parts) > 9 else '')

    data_numeric = np.array(numeric_rows)
    phase_strings = np.array(phase_list, dtype=str)

    pressures = data_numeric[:, 0]
    temps = data_numeric[:, 1]
    densities = data_numeric[:, 2]
    nabla_ad = data_numeric[:, 8]

    # Filter out P=0 rows
    valid = pressures > 0
    pressures = pressures[valid]
    temps = temps[valid]
    densities = densities[valid]
    nabla_ad = nabla_ad[valid]
    phase_strings = np.char.strip(phase_strings[valid])

    # Work in log10 space
    log_p = np.log10(pressures)
    log_t = np.log10(temps)

    unique_log_p = np.unique(log_p)
    unique_log_t = np.unique(log_t)

    n_p = len(unique_log_p)
    n_t = len(unique_log_t)

    # Build 2D grids
    density_grid = np.full((n_p, n_t), np.nan)
    nabla_ad_grid = np.full((n_p, n_t), np.nan)
    phase_grid = np.full((n_p, n_t), '', dtype=object)

    p_idx_map = {v: i for i, v in enumerate(unique_log_p)}
    t_idx_map = {v: i for i, v in enumerate(unique_log_t)}

    for k in range(len(pressures)):
        ip = p_idx_map[log_p[k]]
        it = t_idx_map[log_t[k]]
        density_grid[ip, it] = densities[k]
        nabla_ad_grid[ip, it] = nabla_ad[k]
        phase_grid[ip, it] = phase_strings[k]

    density_interp = RegularGridInterpolator(
        (unique_log_p, unique_log_t),
        density_grid,
        bounds_error=False,
        fill_value=np.nan,
    )
    nabla_ad_interp = RegularGridInterpolator(
        (unique_log_p, unique_log_t),
        nabla_ad_grid,
        bounds_error=False,
        fill_value=np.nan,
    )

    # Per-pressure valid T bounds
    logt_valid_min = np.full(n_p, np.nan)
    logt_valid_max = np.full(n_p, np.nan)
    for ip in range(n_p):
        finite_mask = np.isfinite(density_grid[ip, :])
        if finite_mask.any():
            valid_indices = np.where(finite_mask)[0]
            logt_valid_min[ip] = unique_log_t[valid_indices[0]]
            logt_valid_max[ip] = unique_log_t[valid_indices[-1]]

    # Nearest-neighbor fallback interpolators
    valid_cells = np.isfinite(density_grid)
    ip_valid, it_valid = np.where(valid_cells)
    coords_valid = np.column_stack([unique_log_p[ip_valid], unique_log_t[it_valid]])

    density_nn = NearestNDInterpolator(coords_valid, density_grid[valid_cells])

    nabla_valid = np.isfinite(nabla_ad_grid[valid_cells])
    nabla_ad_nn = NearestNDInterpolator(
        coords_valid[nabla_valid],
        nabla_ad_grid[valid_cells][nabla_valid],
    )

    # Extract liquidus boundary from the phase column.
    # For each pressure row, find the lowest T where phase == 'liquid'.
    liquidus_log_p = []
    liquidus_log_t = []
    for ip in range(n_p):
        liquid_mask = phase_grid[ip, :] == 'liquid'
        if liquid_mask.any():
            first_liquid_idx = np.where(liquid_mask)[0][0]
            liquidus_log_p.append(unique_log_p[ip])
            liquidus_log_t.append(unique_log_t[first_liquid_idx])

    liquidus_log_p = np.array(liquidus_log_p)
    liquidus_log_t = np.array(liquidus_log_t)

    # Precompute grid spacing for O(1) bilinear interpolation.
    # Both PALEOS and Chabrier grids are log-uniform (constant dlogP, dlogT).
    dlog_p = (unique_log_p[-1] - unique_log_p[0]) / (n_p - 1) if n_p > 1 else 1.0
    dlog_t = (unique_log_t[-1] - unique_log_t[0]) / (n_t - 1) if n_t > 1 else 1.0

    # Verify grid is log-uniform (required for O(1) bilinear interpolation)
    if n_p > 2:
        p_spacings = np.diff(unique_log_p)
        if not np.allclose(p_spacings, dlog_p, rtol=1e-3):
            logger.warning(
                f'P grid is not log-uniform: spacing range '
                f'[{p_spacings.min():.6f}, {p_spacings.max():.6f}] '
                f'vs mean {dlog_p:.6f}. Bilinear interpolation may be inaccurate.'
            )
    if n_t > 2:
        t_spacings = np.diff(unique_log_t)
        if not np.allclose(t_spacings, dlog_t, rtol=1e-3):
            logger.warning(
                f'T grid is not log-uniform: spacing range '
                f'[{t_spacings.min():.6f}, {t_spacings.max():.6f}] '
                f'vs mean {dlog_t:.6f}. Bilinear interpolation may be inaccurate.'
            )

    return {
        'type': 'paleos_unified',
        'density_interp': density_interp,
        'nabla_ad_interp': nabla_ad_interp,
        'density_nn': density_nn,
        'nabla_ad_nn': nabla_ad_nn,
        'p_min': 10.0 ** unique_log_p[0],
        'p_max': 10.0 ** unique_log_p[-1],
        't_min': 10.0 ** unique_log_t[0],
        't_max': 10.0 ** unique_log_t[-1],
        'unique_log_p': unique_log_p,
        'unique_log_t': unique_log_t,
        'logt_valid_min': logt_valid_min,
        'logt_valid_max': logt_valid_max,
        'liquidus_log_p': liquidus_log_p,
        'liquidus_log_t': liquidus_log_t,
        'phase_grid': phase_grid,
        # Fast bilinear interpolation data
        'density_grid': density_grid,
        'nabla_ad_grid': nabla_ad_grid,
        'logp_min': unique_log_p[0],
        'logp_max': unique_log_p[-1],
        'logt_min': unique_log_t[0],
        'logt_max': unique_log_t[-1],
        'dlog_p': dlog_p,
        'dlog_t': dlog_t,
        'n_p': n_p,
        'n_t': n_t,
    }